Salvatore wants to construct about 140 apartments, about 7,000 square feet of retail, 120,000 square feet of research space and 50,000 square feet of offices in the Hill on lots that have remained undeveloped for 26 years. He would pay the city $1.25 million for the land.

He stormed out at about 8:30 p.m. after two hours of discussion, when he lost on part of the zoning issue.

Most of the deliberations were devoted to a land-disposition agreement supposed to incorporate agreements on affordable housing and investments in job training, as well as one on parking for events at St. Anthony’s Church.

These had been worked out by a steering committee of citizens led by former aldermanic President Jorge Perez and there was little disagreement with them.

There were some minor changes made by the committee, such as clarifying that New Haven Works would provide the job training and that any sale of the land to a nonprofit would mandate payments in lieu of taxes approved by the alders, rather than by the economic development administrator.

The zone map changes covered several parcels totaling 11.6 acres from BA to BD-3, which would allow for taller buildings and denser development, as well as mixed uses.

There already was an agreement not to change the BA zone for 2 Church St., South, and 35 College St., as they were not part of Salvatore’s plans. The developer, however, whose company is RMS, has said he needed the flexibility of the zone change for the remaining parcels.

The committee voted to take out what has been referred to as Parcel 11, adjacent to Tower One and Tower East, two large apartment complexes for the elderly. The land is now used for parking and Salvatore said that, as of right, he can already build a garage there.

Parcel 11 also borders the more than 200 apartments at Church Street South that will be razed and redeveloped in the near future.

The committee was persuaded not to change the zone after testimony by New Haven Urban Design League President Anstress Farwell and an attorney for Tower One and Tower East, who said his tenants had expressed concern over a high-rise building being constructed on Parcel 11.

He said they preferred a mix of retail and something that would connect them to the rest of the development.

Salvatore said he thought the arrangement worked out by Perez had settled all the questions.

He told the committee that changing the zone would not preclude the kinds of uses the elderly tenants preferred, as he had not settled on what would go on that parcel.

“What we are proposing can be mixed use,” Salvatore said.

The attorney representing the tenants, at a zone-change hearing in November, had submitted testimony in favor of the proposed development, which confused Salvatore because he was now testifying against it.

Salvatore said he never heard from the representative for the Towers since December .

Until the zone change is in place, Salvatore said he could not move forward. He said there would be plenty of time for discussion on the specifics of the deal later.

“It starts here. It doesn’t end here,” he told the committee.

On the affordable-housing aspect, he said he felt optimistic that they could get subsidies for 30 percent to be affordable. He said part of it would be vouchers available from the Church Street South complex, as well as the Choice Neighborhood grant, if it comes through.

There were multiple surprises at the hearing, starting with the fact that there were only two copies of the latest revised land-disposition agreement, which was dated in May, for the committee members to follow. They all had copies of a version dated earlier in April.

Also, Alder Jessica Holmes, D-9, one of the co-chairs of the joint committee, at the outset, said the legislative staff could not find the tape of the December public hearing on the Salvatore project to determine whether it had been closed.

City Plan Director Karyn Gilvarg said that when a zone change is involved, the city has to follow certain protocols. She said she was concerned that additional testimony was being taken, as she thought the hearing had been closed.

The alders’ attorney, Mark Branse, in an email dated Wednesday, sent an opinion to the alders on the public hearing. The city officials at the meeting were unaware of the opinion.

“A motion to table is not the same as a motion to close a public hearing, so it seems clear that the public hearing was not formally closed,” he wrote to the alders. He based this on what appeared in the minutes.

The first announcement of Salvatore’s proposal for the Hill was made in August and came close to falling apart in December, when the joint committee agreed that more public input was needed. At that point the steering committee was put together.

After Salvatore walked out Wednesday, Holmes said: “I would hope that he would continue the conversation. We still have six weeks before it gets voted on by the full board. I feel there has been tremendous progress and it shows a lot of effort both on the part of the developer and the committee.”

The revised agreement now goes to the full Board of Alders on Aug. 1. In the meantime, the joint committee said it would review all the language in the deal and, if other changes needed to be made, it could be amended in August.

The area in the deal is generally bound by Church Street South, Amistad Street, the eastern boundary of Amistad Park, Cedar Street, Minor Street, Howard, Washington and Congress avenues and is close to the Yale School of Medicine and private biotech labs.